Johnson took 3-41 as he looks to stay in shape ahead of the Indian Premier League, but Fremantle’s 174 was beyond the visitors, who replied with just 89 in an 85-run loss in the one day match at Stevens Reserve.
Surprisingly, Australia’s fourth-highest wicket taker did not lead figures for the Roos.
That honour went to Jake Fawcett, who bettered Johnson’s return with 4-18, albeit an effort that took out the tail.
Fawcett landed his second victim via a rare mode of dismissal, claiming Jhye Richardson for hit wicket.
Fremantle looked in trouble at 6-84 but an unbeaten 47 from Joel Crosswell helped guide the side to a defendable total.
Wanneroo’s Rob Richards (46) was the sole shining light in a hapless display from the Roos’ batsmen. The loss dropped the visitors to a season finish of 14th.